A statistical method for high-throughput emergence rate calculation for soybean breeding plots based on field phenotypic characteristics.

Abstract

In the process of smart breeding, the rapid statistics of soybean emergence rate, as an important part of breeding screening, face challenges under environmental constraints, especially the selection and breeding of soybean varieties in dense environments. Due to the influence of environmental factors, the existing methods have shortcomings, such as low throughput, low efficiency, and insufficient precision. Therefore, an effective and precise statistical method is required. In this study, UAV (Unmanned Aerial Vehicle)-scale data combined with ground measurement data were used as the research object to explore the feasibility of improving the throughput, efficiency, and accuracy of breeding screening under intensive soybean planting. To this end, a set of technical solutions, including background removal, object detection, and accurate counting, were designed. Firstly, a combined background segmentation method based on contrast enhancement filtering combined with ultra-green eigenvalues and the Otsu algorithm was proposed to remove the complex background in remote sensing images and retain the morphological information of soybean seedlings. Secondly, the deep learning object detection model was used to infer and predict the processed images to label soybean seedlings. Then, a soybean seedling counting algorithm was constructed: by establishing a soybean seedling growth model, the idea of "growth normalization" was proposed, and the expansion-compression factor was defined to eliminate the influence of soybean seedling growth inconsistency on counting. After statistical and in-depth analysis of the growth and planting characteristics of soybean seedlings under overlapping conditions, the "inter-seedling occlusion counting algorithm" was proposed to solve the problem of overlapping counting between seedlings. In order to solve the problem of an overlapping bounding box, a soft strategy is specially designed to avoid the redundant values brought by it. Finally, according to the calculation results, the statistical thematic map of soybean emergence rate based on plot plots was displayed. After experiments, the proposed method can effectively count the number of soybean seedlings in the image, with an overall accuracy of 99.18% and an error rate of 0.82%. In addition, Yolov8n had the best recognition effect in the soybean seedling detection task, with a mAP (0.5-0.95) of 85.15%. The proposed background segmentation method increased the mAP (0.5-0.95) of the detection results by 4.06%. It has been demonstrated through experimental tests and verifications that solid support for the statistical work concerning the soybean emergence rate under the condition of intensive planting is provided by this method. This innovative method has played a facilitating role in accelerating the breeding process and has also provided some new ideas and reference directions for further exploration of efficient screening.

Plant phenotyping relevance

大豆苗の出芽率を高スループットに推定するため、画像分割・物体検出・重複個体計数を開発し、精度検証まで行った植物フェノタイピング手法研究である。

Code and data availability

The paper describes UAV imagery of soybean breeding plots and a YOLOv8n-based counting pipeline, but the Data availability statement explicitly says no datasets were generated or analysed, and no code, model weights, or data repository is mentioned anywhere in the supplied blocks. No paper-specific public asset exists.

No evidence-backed public reproduction asset is currently recorded.